During April, May and August 2005 intensive field investigations were undertaken to characterize the physical limnology of Winam Gulf and Rusinga Channel regions of Lake Victoria in Kenya. Both the field data and numerical simulations with the three-dimensional (3D) hydrodynamics model, ELCOM (Estuary, Lake and Coastal Ocean Model), during these two field studies led to two major conclusions. First, though water currents in Rusinga Channel can be quite large (ca. 10-50 cm s-1), exchange through the channel is low because the tidal-like oscillations result in low net transport over a 24 hour period. Second, Winam Gulf can be segmented into four regions, two of which have relatively low flushing rates as compared to time scales of biogeochemical processing. Regionally, on the basis of these physical limological findings the implications for water quality management strategies for Winam Gulf are presented. Internationally, the role of Winam Gulf as a net source or sink of nutrients and pollutants to the open waters of Lake Victoria is addressed.